Officials say a half-dozen heart attack deaths were linked to the fire.
"Causation was proved, the trauma of the fire, the stress of the fire caused these individuals to die of a medical condition, specifically heart attacks," said San Bernardino County District Attorney Michael Ramos.
Fowler is currently serving time in Lancaster State Prison for burglary, but he'll be transferred back to San Bernardino to face these new charges.
The Old Fire started along Highway 18 in the Waterman Canyon area of the San Bernardino Mountains and eventually swept across 91,000 acres, or about 140 square miles. It was among the most destructive fires in San Bernardino County history.
"Our hearts go out to the thousands of people affected by this horrific fire, who are continued to be affected by this fire in their loss of homes. Some people not able to build their homes even to this date," said Ramos. "Although justice was delayed, I will tell you justice will not be denied in this case."
More than 30 communities were evacuated during the blaze, and 983 structures were destroyed. The total loss of property was more than $170 million.
Two months after the massive fire, 14 people were killed on Christmas Day when heavy rain sent a massive flow of debris-laden runoff down Waterman Canyon, sweeping away a church camp.
Fowler was first interviewed in connection with the fire in February 2004 based on a telephone tip, but there was not enough evidence, Deputy District Attorney Vic Stull said.
The statute of limitations on arson would have run out on Oct. 25.
Fowler's arraignment is expected within two weeks.
The Associated Press contributed to this report.